Assessing the measurement transfer function of single-cell RNA sequencing
Assessing the measurement transfer function of single-cell RNA sequencing
Abstract Recently, measurement of RNA at single cell resolution has yielded surprising insights. Methods for single-cell RNA sequencing (scRNA-seq) have received considerable attention, but the broad reliability of single cell methods and the factors governing their performance are still poorly known. Here, we conducted a large-scale control experiment to assess the transfer function of three scRNA-seq methods and factors modulating the function. All three methods detected greater than 70% of the expected number of genes and had a 50% probability of detecting genes with abundance greater than 2 to 4 molecules. Despite the small number of molecules, sequencing depth significantly affected gene detection. While biases in detection and quantification were qualitatively similar across methods, the degree of bias differed, consistent with differences in molecular protocol. Measurement reliability increased with expression level for all methods and we conservatively estimate the measurement transfer functions to be linear above ~5-10 molecules. Based on these extensive control studies, we propose that RNA-seq of single cells has come of age, yielding quantitative biological information.
Chow Robert H.、Camarena Adrian、Ai Rizi、Ding Bo、Zhang Kun、Evgrafov Oleg V.、Fan Jian-Bing、Fisher Stephen A.、Hernstein Jennifer S.、Kim Jae Mun (Hugo)、Liu Rui、Souaiaia Tade、Walker Chris P.、Wang Jinhui、Wang Wei、Wilberg Andre、Zheng Lina、Lin Ming-Yi、Wang Kai、Salathia Neeraj、Kim Junhyoung、Dominguez Reymundo、Eberwine James、Knowles James A.、Kim Tae Kyung、McGroty Sean、Nguyen Joseph、Shallcross Jamie、Dueck Hannah R.、Mack William J.、Spaethling Jennifer
Department of Physiology & Biophysics, Zilkha Neurogenetic Institute, University of Southern CaliforniaDepartment of Psychiatry & The Behavioral Sciences, Keck School of Medicine, University of Southern CaliforniaDepartment of Chemistry and Biochemistry, University of California at San DiegoDepartment of Chemistry and Biochemistry, University of California at San DiegoDepartment of Bioengineering, University of California at San DiegoDepartment of Psychiatry & The Behavioral Sciences, Keck School of Medicine, University of Southern CaliforniaIllumina, Inc.Department of Biology, School of Arts and SciencesDepartment of Psychiatry & The Behavioral Sciences, Keck School of Medicine, University of Southern CaliforniaDepartment of Psychiatry & The Behavioral Sciences, Keck School of Medicine, University of Southern CaliforniaDepartment of Bioengineering, University of California at San DiegoDepartment of Psychiatry & The Behavioral Sciences, Keck School of Medicine, University of Southern CaliforniaDepartment of Psychiatry & The Behavioral Sciences, Keck School of Medicine, University of Southern CaliforniaDepartment of Pharmacology, Perelman School of Medicine, University of PennsylvaniaDepartment of Chemistry and Biochemistry, University of California at San DiegoDepartment of Chemistry and Biochemistry, University of California at San DiegoDepartment of Chemistry and Biochemistry, University of California at San DiegoDepartment of Physiology & Biophysics, Zilkha Neurogenetic Institute, University of Southern CaliforniaDepartment of Psychiatry & The Behavioral Sciences, Keck School of Medicine, University of Southern CaliforniaIllumina, Inc.Department of Biology, School of Arts and SciencesDepartment of Physiology & Biophysics, Zilkha Neurogenetic Institute, University of Southern CaliforniaDepartment of Pharmacology, Perelman School of Medicine, University of PennsylvaniaDepartment of Psychiatry & The Behavioral Sciences, Keck School of Medicine, University of Southern CaliforniaDepartment of Pharmacology, Perelman School of Medicine, University of Pennsylvania||Allen Institute for Brain ScienceDepartment of Biology, School of Arts and SciencesDepartment of Psychiatry & The Behavioral Sciences, Keck School of Medicine, University of Southern CaliforniaDepartment of Biology, School of Arts and SciencesDepartment of Genomics and Computational Biology, Perelman School of Medicine, University of PennsylvaniaDepartment of Neurological Surgery, Zilkha Neurogenetic InstituteDepartment of Pharmacology, Perelman School of Medicine, University of Pennsylvania
生物科学研究方法、生物科学研究技术分子生物学细胞生物学
Chow Robert H.,Camarena Adrian,Ai Rizi,Ding Bo,Zhang Kun,Evgrafov Oleg V.,Fan Jian-Bing,Fisher Stephen A.,Hernstein Jennifer S.,Kim Jae Mun (Hugo),Liu Rui,Souaiaia Tade,Walker Chris P.,Wang Jinhui,Wang Wei,Wilberg Andre,Zheng Lina,Lin Ming-Yi,Wang Kai,Salathia Neeraj,Kim Junhyoung,Dominguez Reymundo,Eberwine James,Knowles James A.,Kim Tae Kyung,McGroty Sean,Nguyen Joseph,Shallcross Jamie,Dueck Hannah R.,Mack William J.,Spaethling Jennifer.Assessing the measurement transfer function of single-cell RNA sequencing[EB/OL].(2025-03-28)[2025-08-02].https://www.biorxiv.org/content/10.1101/045450.点此复制
评论